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- PDB-6qn4: Death-associated Protein Kinase 1 (DAPK1) catalytic and auto-regu... -

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Basic information

Entry
Database: PDB / ID: 6qn4
TitleDeath-associated Protein Kinase 1 (DAPK1) catalytic and auto-regulatory domains with S289E and S308E mutations
ComponentsDeath-associated protein kinase 1
KeywordsSIGNALING PROTEIN / kinase / apoptosis / autophagy / CaMK
Function / homology
Function and homology information


cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / syntaxin-1 binding / extrinsic apoptotic signaling pathway via death domain receptors ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / regulation of NMDA receptor activity / calcium/calmodulin-dependent protein kinase activity / syntaxin-1 binding / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / protein autophosphorylation / regulation of apoptotic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / calmodulin binding / postsynaptic density / regulation of autophagy / negative regulation of translation / intracellular signal transduction / protein phosphorylation / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / GTP binding / glutamatergic synapse / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuart, A.-S. / Wilmanns, M.
CitationJournal: To Be Published
Title: Molecular mechanisms behind DAPK regulation: how phosphorylation switches work
Authors: Huart, A.-S. / Simon, B. / Lubner, J. / Mertens, H.D.T. / Temmerman, K. / Hoffmann, J.-E. / Svergun, D.I. / Schwartz, D. / Schultz, C. / Wilmanns, M.
History
DepositionFeb 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Death-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,85513
Polymers36,0501
Non-polymers80512
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-13 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.374, 77.478, 99.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Death-associated protein kinase 1 / DAP kinase 1


Mass: 36050.250 Da / Num. of mol.: 1 / Mutation: S289E S308E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK1, DAPK / Production host: Escherichia coli (E. coli)
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.64 % / Description: plate needle
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop
Details: 16% PEG 4000, 0.1 M Tris pH 8.5, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→99.931 Å / Num. obs: 26520 / % possible obs: 99.9 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.093 / Rrim(I) all: 0.161 / Net I/σ(I): 7.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.4 % / Num. unique obs: 1440 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimlessdata scaling
Coot0.8.6model building
PHENIX1.9-1692refinement
PHASERPhenix 1.9-1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B4L

4b4l


Resolution: 2.5→61.23 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 30.65
RfactorNum. reflection% reflection
Rfree0.2661 1194 4.88 %
Rwork0.2149 --
obs0.2173 24450 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→61.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 53 34 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092330
X-RAY DIFFRACTIONf_angle_d0.9473133
X-RAY DIFFRACTIONf_dihedral_angle_d4.1521396
X-RAY DIFFRACTIONf_chiral_restr0.054344
X-RAY DIFFRACTIONf_plane_restr0.007406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.60020.37231170.34892569X-RAY DIFFRACTION99
2.6002-2.71850.33931410.30762548X-RAY DIFFRACTION100
2.7185-2.86180.31251360.27862600X-RAY DIFFRACTION100
2.8618-3.04110.34851440.25722584X-RAY DIFFRACTION100
3.0411-3.27590.31031550.22572546X-RAY DIFFRACTION100
3.2759-3.60560.31551060.20682641X-RAY DIFFRACTION100
3.6056-4.12720.21031350.17412582X-RAY DIFFRACTION100
4.1272-5.19940.21561230.17692598X-RAY DIFFRACTION100
5.1994-61.24880.25311370.2162588X-RAY DIFFRACTION100

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